Brake pedal sits too low

As far as I know, the master cylinder is fine. It is new and I just bench bled it last night after a little mishap in which the pushrod pulled the piston partway out of the bore (I was gently pulling on the pedal after I saw it was sitting low). I am currently replacing a wheel cylinder, so I cannot test it inside the vehicle until that is complete. After the piston came out (not even past the first seal) I gently pushed it back in and removed the master cylinder to bleed it. I don't think that cause any damage, and it returns to the regular position after it is depressed.